Personal summary
I am a computational biologist working on understanding the forces that govern the interactions between organisms in ecologically critical environments, such as coral reefs, and the forces that drive major evolutionary transitions, such as the one that gave rise to the first photosynthetic Eukaryotas.
Contact information
| left | Left |
|---|---|
| Department of Biochemistry and Microbiology, Rutgers University, USA | |
| ts942@sebs.rutgers.edu | |
| timothystephens.github.io | |
| TimothyStephens | |
| @timstep1383 |
Education
| year | what |
|---|---|
| 2016 — 2019 | PhD, Institute for Molecular Bioscience, The University of Queensland |
| 2015 | Honours, Institute for Molecular Bioscience, The University of Queensland |
| 2012 — 2015 | Bachelor of Biotechnology, Institute for Molecular Bioscience, The University of Queensland |
Research Experience
| year | what |
|---|---|
| 2019 — present | Post Doctoral Associate, Department of Biochemistry and Microbiology, Rutgers University |
| 2016 — 2019 | PhD, Institute for Molecular Bioscience, The University of Queensland |
| 2015 | Honours Project, Institute for Molecular Bioscience, The University of Queensland |
| 2014 | Undergraduate Researcher Project, School of Biological Sciences, The University of Queensland |
| 2013 | Paid Research Assistant, School of Biological Sciences, The University of Queensland |
| 2012 — 2013 | Undergraduate Research Project, Institute for Molecular Bioscience, The University of Queensland |
Teaching experience
| year | what |
|---|---|
| 2020 — present | Guest lecturer Rutgers University Design and conducted lectures on de novo next-generation genome and transcriptome sequencing, metabolomics, proteomics, metagenomics, phylogenetics, and phylogenomics in a join undergraduate and postgraduate course titled “Fundamentals of Microbial Genomics”. Duties include designing and marking student’ exam questions and oral presentations. |
| 2018 | Head Practical Tutor University of Queensland Duties included designing and developing assessment material for the course and organising marking of assignments. |
| 2016 — 2017 | Practical Tutor University of Queensland Duties included assisting students with the completion of set questions and marking of assignments. |
| 2013 | Science Mentor University of Queensland Duties included organizing and running first year science student introduction and social engagement events designed to inform students about study/research opportunities available at The University of Queensland. |
| 2013 — 2014 | Peer Assisted Study Session (PASS) Tutor University of Queensland Duties included planning and leading multiple weekly tutorial sessions, each comprising 20-30+ students. |
| 2012 — 2014 | CASPiE Tutor University of Queensland Duties included guiding undergraduate chemistry students through an advanced set of research-focused practicals, with the aim of developing their critical and experimental thinking. |
Professional development
| year_begin | what |
|---|---|
| 2017 | Research Commercialisation Workshop, University of Queensland |
| 2017 | UQ Idea Hub, University of Queensland |
Awards and honours
| year_begin | what |
|---|---|
| 2021 | 2019 Dean’s Award for Outstanding Higher Degree by Research Theses, University of Queensland |
| 2018 | Registration award for Society for Molecular Biology & Evolution (SMBE) 2018, SMBE |
| 2017 | Won best pitch prize at the UQ Idea Hub, University of Queensland |
| 2016 | Research Training Program (RTP) scholarship, University of Queensland |
| 2016 | Top poster prize at the IMB Research Higher Degree Student Symposium, University of Queensland |
| 2012 | Selected for the Advanced Study Program in Science (ASPinS; based on academic merit), University of Queensland |
| 2012 | Dean’s Commendation for Academic Excellence (achieved a GPA over 6.6), University of Queensland |
| 2011 | Merit Scholarship for academic achievement, University of Queensland |
Publications
| year | ref2print |
|---|---|
| 2023 | *Williams A., *Stephens T. G., Shumaker A., and Bhattacharya D. Peeling back the layers of coral holobiont multi-omics data. iScience, 2023. *Co-first authorship |
| 2023 | Stephens T. G., Strand E. L., Putnam H. M., and Bhattacharya D. Ploidy variation and its implications for reproduction and population dynamics in two sympatric Hawaiian coral species. Genome Biology and Evolution, evad149, 2023. [Preprint] [URL] |
| 2023 | Etten J. V, Stephens T. G., and Bhattacharya D. A k-mer-based approach for inferring phylogenetic relatedness of environmental genomic data. Systems Biology, syad037, 2023. [URL] |
| 2023 | Etten J. V., Benites F. L., Stephens T. G., Yoon H. S., and Bhattacharya D. Algae obscura: The potential of rare species as model systems. Journal of Phycology, 59(2):293-300, 2023. [URL] |
| 2022 | Stephens T. G., Lee J., Jeong Y., Yoon H. S., Putnam H. M., Majerova E., and Bhattacharya D. High-quality genome assemblies from key Hawaiian coral species. GigaScience, 11:giac098, 2022. [URL] |
| 2022 | Benites L. F., Stephens T. G., and Bhattacharya D. Multiple waves of viral invasions in Symbiodiniaceae algal genomes. Virus Evolution, 8:veac101, 2022. [Preprint] [URL] |
| 2022 | Bhattacharya D., Etten J. V., Benites L. F., and Stephens T. G. Endosymbiotic ratchet accelerates divergence after organelle origin. BioEssays, e2200165, 2022. [URL] |
| 2022 | *Gabr A., *Stephens T. G., and Bhattacharya D. Loss of key endosymbiont genes may facilitate early host control of the chromatophore in Paulinella. iScience, 25:104974, 2022. [URL] *Co-first authorship |
| 2022 | Meng Z., Williams A., Liau P., Stephens T. G., Drury C., Chiles E. N., Su X., Javanmard M., and Bhattacharya D. Development of a portable toolkit to diagnose coral thermal stress. Scientific Reports, 12:14398, 2022. [URL] |
| 2022 | Bhattacharya D., Stephens T. G., Tinoco A., Richmond R., and Cleves P. A. Life on the edge: Hawaiian model for coral evolution. Limnology and Oceanography, 67:1976-1985, 2022. [URL] |
| 2022 | *Calatreva V., *Stephens T. G., Gabr A., Grossman A. R., and Bhattacharya D. Retrotransposition facilitated the establishment of a primary plastid in the thecate amoeba Paulinella. PNAS, 119:e2121241119, 2022. [URL] *Co-first authorship |
| 2022 | *Gabr A., *Stephens T. G., and Bhattacharya D. Hypothesis: Trans-splicing generates evolutionary novelty in the photosynthetic amoeba Paulinella. Journal of Phycology, 58:392-405, 2022. [URL] *Co-first authorship |
| 2022 | Dougan K. E., Gonzalez-Pech R. A., Stephens T. G., Shah S., Chen Y., Ragan M. A., Bhattacharya D., and Chan C. X. Genome-powered classification of microbial eukaryotes: focus on coral algal symbionts. Trends in Microbiology, 30:831-840, 2022. [URL] |
| 2022 | Gabr A., Zournas A., Stephens T. G., Dismukes G., and Bhattacharya D. Evidence for a robust photosystem II in the photosynthetic amoeba Paulinella. New Phytologist, 234:934-945, 2022. [URL] |
| 2021 | Williams A., Pathmanathan J. S., Stephens T. G., Su X., Chiles E. N., Conetta D., Putnam H. M., and Bhattacharya D. Multi-omic characterization of the thermal stress phenome in the stony coral Montipora capitata. PeerJ, 9:e12335, 2021. [Preprint] [URL] |
| 2021 | Stephens T. G., Gabr A., Calatreva V., Grossman A. R., and Bhattacharya D. Why is primary endosymbiosis so rare?. New Phytologist, 231:1693-1699, 2021. [URL] |
| 2021 | Bernard G., Stephens T. G., Gonzalez-Pech R. A., and Chan C. X. Inferring phylogenomic relationship of microbes using scalable alignment-free methods. Methods in Molecular Biology, 2242:69-76, 2021. [URL] |
| 2021 | Jacobus A. P., Stephens T. G., Youssef P., Gonzalez-Pech R., Ciccotosto-Camp M. M., Dougan K. E., Chen Y., Basso L. C., Frazzon J., Chan C. X., and Gross J. Comparative genomics supports that Brazilian bioethanol Saccharomyces cerevisiae comprise a unified group of domesticated strains related to cachaca spirit yeasts. Frontiers in Microbiology, 12:644089, 2021. [Preprint] [URL] |
| 2021 | Gonzalez-Pech, R. A., Stephens T. G., Chen Y., Mohamed A. R., Cheng Y., Shah S., Dougan K. E., Fortuin M. D. A., Lagorce R., Burt D. W., Bhattacharya D., Ragan M. A., and Chan C. X. Comparison of 15 dinoflagellate genomes reveals extensive sequence and structural divergence in family Symbiodiniaceae and genus Symbiodinium. BMC Biology, 0.842361111, 2021. [Preprint] [URL] |
| 2020 | Lhee D., Lee J., Ettahi K., Cho C. H., Ha J., Chan Y., Zelzion U., Stephens T. G., Price D. C., Gabr A., Nowack E. C. M., Bhattacharya D., and Yoon H. S. Amoeba genome reveals dominant host contribution to plastid endosymbiosis. Molecular Biology and Evolution, 38:344-357, 2020. [URL] |
| 2020 | Stephens T. G., Gonzalez-Pech R. A., Cheng Y., Mohamed A. R., Burt D. W., Bhattacharya D., Ragan M. A., and Chan C. X. Genomes of the dinoflagellate Polarella glacialis encode tandemly repeated single-exon genes with adaptive functions. BMC Biology, 18:56, 2020. [Preprint] [URL] Featured by IMB News |
| 2019 | Chen Y., Gonzalez-Pech R. A., Stephens T. G., Bhattacharya D., and Chan C. X. Evidence that inconsistent gene prediction can mislead analysis of dinoflagellate genomes. Journal of Phycology, 56:6-10, 2019. [Preprint] [URL] |
| 2018 | *Gonzalez-Pech R. A., *Stephens T. G., and Chan C. X. Commonly misunderstood parameters of NCBI BLAST and important considerations for users. Bioinformatics, 35:2697-6998, 2018. [URL] *Co-first authorship [F1000 recommended] |
| 2018 | Stephens T. G., Ragan M. A., Bhattacharya D., and Chan C. X. Core genes in diverse dinoflagellate lineages include a wealth of conserved dark genes with unknown functions. Scientific Reports, 8:17175, 2018. [URL] |
| 2018 | Liu H., Stephens T. G., Gonzalez-Pech R. A., Beltran V. H., Lapeyre B., Bongaerts P., Cooke I., Aranda M., Bourne D. G., Foret S., Miller D. J., van Oppen M. J. H., Voolstra C. R., Ragan M.A., and Chan C.X. Symbiodinium genomes reveal adaptive evolution of functions related to coral-dinoflagellate symbiosis. Communications Biology, 0.107638889, 2018. [Preprint] [URL] Featured by multiple outlets: IMB News, GBRF, Video Feature, IMB 2018 year in review |
| 2018 | Lee J, Yang E. C., Graf L., Yang J. H., Qiu H., Zelzion U., Chan C. X., Stephens T. G., Weber A. P. M., Boo G. H., Boo S. M., Kim K. M., Shin Y., Jung M., Lee S. J., Yim H. S., Lee J. Y., Bhattacharya D., and Yoon H. S. Analysis of the draft genome of the red seaweed Gracilariopsis chorda provides insights into genome size evolution in Rhodophyta. Molecular Biology and Evolution, 35:1869-1886, 2018. [URL] |
| 2016 | Stephens T. G., Bhattacharya D., Ragan M. A., and Chan C. X. PhySortR: a fast, flexible tool for sorting phylogenetic trees in R. PeerJ, 4:e2038, 2016. [Preprint] [URL] |
Talks
| year_begin | what |
|---|---|
| 2023 | Stephens T. G., Chille E., Wong K., Andrade N., Hulett R., Cleves P., Bhattacharya D., Traylor-Knowles N. Shining a light on “dark” proteins in corals. From Postdoc to Principal Investigator: An NSF Division of Integrative Organismal Systems (IOS) Virtual Colloquium 2023. 13-14th September 2023, Virtual. |
| 2023 | Stephens T. G., Calatrava V., Gabr A., Grossman A., and Bhattacharya D. Exploring the origin and evolution of primary plastids using Paulinella as a model system. International Society of Endocytobiology conference 2023. 10-14th September 2023, Field Museum, Chicago, 2023. |
| 2023 | Stephens T. G., Chille E., Strand E. L., Putnam H. M., and Bhattacharya D. Multi-omics investigation of coral resilience. Invited talk at Carnegie Plant Biology Seminar, August 2023. 25th August 2023, Carnegie Department of Plant Biology, Stanford University, USA. |
| 2023 | Stephens T. G., Calatrava V., Gabr A., Grossman A., and Bhattacharya D. Exploring the origin and evolution of primary plastids using Paulinella as a model system. New Phytologist Next Generation Scientists Conference 2023. 3rd July 2023, National University of Singapore, Singapore. |
| 2023 | Stephens T. G., Calatrava V., Gabr A., Grossman A., and Bhattacharya D. Exploring endosymbiosis and biotic interactions using niche, non-model algae. Invited talk at SCMB GenGen/ACE Special Seminar. 10th January 2023, The University of Queensland, Brisbane, Australia. |
| 2022 | Stephens T. G., Williams A., Shumaker A., and Bhattacharya D. Integration of multi-omics coral data under thermal stress . 4th Institute for Food, Nutrition, and Health. 4th November 2022, Rutgers University, New Jersey, USA. |
| 2022 | Stephens T. G., Strand E. L., Putnam H. M., and Bhattacharya D. Differences in ploidy and the prevalence of clonal propagation between Montipora capitata and Pocillopora acuta from Kane’ohe Bay, Hawai’i. 15th International Coral Reef Symposium. 3-8th July 2022, Bremen, Germany. |
| 2022 | Stephens T. G., Etten J. V., McDermott T., and Bhattacharya D. Analysis of environmental meta-omics data from the extremophilic red algae Cyanidiophyceae. Joint Aquatic Sciences Meeting. 14-20th May, 2022, Grand Rapids, USA. |
| 2021 | Stephens T. G., Calatrava V., Gabr A., Grossman A., and Bhattacharya D. Insights into the evolution of a primary endosymbiosis through analysis of the Paulinella genome. 75th Annual Meeting of the Phycological Society of America. 13-22nd July 2021, online. |
| 2021 | Stephens T. G., Calatrava V., Gabr A., Grossman A., and Bhattacharya D. Insights into the evolution of a primary endosymbiosis through analysis of the Paulinella genome. 12th International Phycological Congress. 22-26th March 2021, Chile. |
| 2019 | Stephens T. G., Bhattacharya D., Ragan M. A., and Chan C. X. Polarella genomics: understanding the evolutionary transition to algal symbiosis and cold adaptation. Joint Academic Microbiology Seminars (JAMS). 9th April 2019, Brisbane, Australia. |
| 2018 | Stephens T. G., Bhattacharya D., Ragan M. A., and Chan C. X. Polarella genomics: understanding the evolutionary transition to algal symbiosis and cold adaptation. Botany Department, Biosciences Institute, University of Sao Paulo. 14th December 2018, Sao Paulo, Brazil. |
| 2018 | Stephens T. G., Bhattacharya D., Ragan M. A., and Chan C. X. Polarella genomics: understanding the evolutionary transition to algal symbiosis and cold adaptation. 2nd Bioenergy Workshop, UNESP-USP-UNICAMP Integrated Postgraduate Program in Bioenergy, Institute for Research in Bioenergy, State University of Sao Paulo (UNESP). 6th December 2018, Sao Paulo, Brazil. |
| 2017 | Stephens T. G., Bhattacharya D., Ragan M. A. and Chan C. X. Insights into coral reef symbiosis from the genome of cold-adapted algae. EMBL Australia Postgraduate Symposium 2017, 29th November-1st December 2017, Sydney, Australia. |
Poster presentations
| year_begin | what |
|---|---|
| 2023 | Stephens T. G., Chille E., Wong K., Andrade N., Hulett R., Cleves P., Bhattacharya D., Traylor-Knowles N. Shining a light on “dark” proteins in corals. NSF EDGE PI Meeting 2023. 10-11th October 2023, Alexandria, Virginia, USA. |
| 2023 | Stephens T. G., Calatrava V., Gabr A., Grossman A., and Bhattacharya D. Exploring the origin and evolution of primary plastids using Paulinella as a model system. JGI Annual User Meeting 2023. 21-24th August 2023, JGI, Berkeley, California, USA. |
| 2018 | Stephens T. G., Bhattacharya D., Ragan M. A., and Chan C. X. Polarella genomics: understanding cold adaptation and evolutionary transition to symbiosis in dinoflagellates. Society for Molecular Biology & Evolution (SMBE) annual meeting 2018, 8-12th July 2018, Yokohama, Japan. |
| 2016 | Stephens T. G., Chan C. X., and Ragan M. Polarella genomics: understanding the evolutionary transition to algal symbiosis and cold adaptation, IMB Research Higher Degree Student Symposium, 13th Jul 2016, The University of Queensland, Brisbane, Australia. |
Grants
| year_begin | what |
|---|---|
| 2023 | Rutgers TechAdvance Fund, $74,842 USD Funds to continue development of our coral health monitoring toolkit. Principal Investigators: Debashish Bhattacharya (Rutgers University), Rutgers University |
| 2023 | Core Facility Utilization Application, $5,000 USD Funds for metabolomic profiling of the sex hormone cycle in spawning corals. Principal Investigators: Debashish Bhattacharya (Rutgers University), Rutgers University |
| 2022 | Core Facility Utilization Application, $5,000 USD Funds for sequencing of coral microbiome samples. Principal Investigators: Debashish Bhattacharya (Rutgers University), Rutgers University |
| 2022 | Center for Nutrition, Microbiome, and Health Small Grant FY-22, $2,000 USD Characterizing the coral microbiome biogeography across colonies and reefs. Principal Investigators: Debashish Bhattacharya (Rutgers University), Center for Nutrition, Rutgers University |
| 2018 | UQ-FAPESP Strategic Research Fund SPRINT (2018/15159-9), $20,000 (~USD $14,000) Integrated genomic approaches to understand stress tolerance in bioethanol-producing yeasts and coral reef symbionts Principal Investigators: Cheong Xin Chan (UQ) and Jeferson Gross (State University of Sao Paulo), Jointly funded by University of Queensland (UQ) and Sao Paulo State Foundation (FAPESP) |
Media coverage
| year_begin | what |
|---|---|
| 2022 | Our paper Retrotransposition facilitated the establishment of a primary plastid in the thecate amoeba Paulinella covered by Rutgers Research |
| 2022 | Article by Rutgers Research on our short film The Coral Holobiont Response to Climate Change which won Best Trailer in the Kiez Berlin Film Festival. |
| 2021 | Our paper Why is primary endosymbiosis so rare? was covered by Rutgers Newsroom. We also produced two animated videos: Video 1, Video 2 |
| 2020 | Our paper Amoeba Genome Reveals Dominant Host Contribution to Plastid Endosymbiosis covered by Rutgers Today |